Bioinformatics. 2010 Aug 1;26(15):1915-7. Epub 2010 Jun 15.

ViewDock TDW: high-throughput visualization of virtual screening results.

Lau CD, Levesque MJ, Chien S, Date S, Haga JH.

Source

Department of Bioengineering, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

Abstract

SUMMARY: ViewDock TDW is a modification of the pre-existing ViewDock Chimera extension (http://www.cgl.ucsf.edu/chimera/) used to visualize results of virtual screening experiments. By combing TDW hardware and an enhanced ViewDock interface, dozens of ligand-protein complexes are rendered simultaneously to parallelize the analysis of candidate ligands. The ViewDock TDW GUI allows the user to easily and interactively manipulate the molecules on the TDW as an entire set, a selected subset or a single ligand-protein complex and preserves all Chimera functionality. Availability and Implementation: ViewDock TDW is an open source software; freely available on the web at http://www.tdw-prime.webs.com. Chimera UCSF is also available, free of charge, at http://www.cgl.ucsf.edu/chimera/

PMID:: 20551133; [PubMed - indexed for MEDLINE]
PMCID: PMC2905552

Free PMC Article

Images from this publication.See all images (1) Free text

Publication Types, MeSH Terms, Substances, Grant Support

Publication Types

MeSH Terms

Substances

Grant Support

P41 RR-01081/RR/NCRR NIH HHS/United States

LinkOut - more resources

Full Text Sources

Supplemental Content

Related citations

UCSF Chimera--a visualization system for exploratory research and analysis. [J Comput Chem. 2004]
UCSF Chimera--a visualization system for exploratory research and analysis.
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct; 25(13):1605-12.
VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters. [Bioinformatics. 2010]
VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters.
Prakhov ND, Chernorudskiy AL, Gainullin MR. Bioinformatics. 2010 May 15; 26(10):1374-5. Epub 2010 Apr 8.
LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. [Bioinformatics. 2009]
LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.
Ryan M, Diekhans M, Lien S, Liu Y, Karchin R. Bioinformatics. 2009 Jun 1; 25(11):1431-2. Epub 2009 Apr 15.
MODBASE, a database of annotated comparative protein structure models, and associated resources. [Nucleic Acids Res. 2004]
MODBASE, a database of annotated comparative protein structure models, and associated resources.
Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, et al. Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D217-22.
Review Free resources to assist structure-based virtual ligand screening experiments. [Curr Protein Pept Sci. 2007]
Review Free resources to assist structure-based virtual ligand screening experiments.
Villoutreix BO, Renault N, Lagorce D, Sperandio O, Montes M, Miteva MA. Curr Protein Pept Sci. 2007 Aug; 8(4):381-411.

See reviews... See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Free in PMC
Free full text articles in PMC

Recent activity

Clear Turn Off Turn On

ViewDock TDW: high-throughput visualization of virtual screening results.
ViewDock TDW: high-throughput visualization of virtual screening results.
Bioinformatics. 2010 Aug 1 ;26(15):1915-7. Epub 2010 Jun 15 .

PubMed
Inhibition and binding kinetics of the hepatitis C virus NS3 protease inhibitor ...
Inhibition and binding kinetics of the hepatitis C virus NS3 protease inhibitor ITMN-191 reveals tight binding and slow dissociative behavior.
Biochemistry. 2009 Mar 24 ;48(11):2559-68.

PubMed
A pentatricopeptide repeat protein facilitates the trans-splicing of the maize c...
A pentatricopeptide repeat protein facilitates the trans-splicing of the maize chloroplast rps12 pre-mRNA.
Plant Cell. 2006 Oct ;18(10):2650-63. Epub 2006 Oct 13 .

PubMed
Chronic polyneuropathy and Lyme disease.
Chronic polyneuropathy and Lyme disease.
Eur J Neurol. 2006 Nov ;13(11):1213-5.

PubMed
Type 1-polarized dendritic cells loaded with autologous tumor are a potent immun...
Type 1-polarized dendritic cells loaded with autologous tumor are a potent immunogen against chronic lymphocytic leukemia.
J Leukoc Biol. 2008 Jul ;84(1):319-25. Epub 2008 Apr 21 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: